Feature/add db serialisation conformance test (#311)

* add test for feeder_audit with multimedia and locatable attributes * add test for locatable attributes on element. * fix action double serialization of workflow_id and guideline_id see CDR-44 * add test for section see CDR-44 * add DbConformanceTest see CDR-44 * edit CHANGELOG.md see CDR-44 * added test for null_reason see CDR-44
ehrbase · Feb 2, 2022 · 33fcf39 · 33fcf39
1 parent 762ecca
commit 33fcf39
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Showing 16 changed files with 892 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ Note: version releases in the 0.x.y range may introduce breaking changes.
 - cleanup created templates (https://github.com/ehrbase/openEHR_SDK/issues/298)
 - WebTemplate based validation (see https://github.com/ehrbase/openEHR_SDK/pull/309)
 - flat: created conformance tests (see https://github.com/ehrbase/openEHR_SDK/pull/310; https://github.com/ehrbase/openEHR_SDK/pull/305; https://github.com/ehrbase/openEHR_SDK/pull/304; https://github.com/ehrbase/openEHR_SDK/pull/301) 
+- db-serialising: created conformance test (see https://github.com/ehrbase/openEHR_SDK/pull/311) 
 
 ### Fixed
 

diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/attributes/ActionAttributes.java b/serialisation/src/main/java/org/ehrbase/serialisation/attributes/ActionAttributes.java
@@ -40,14 +40,6 @@ public ActionAttributes(CompositionSerializer compositionSerializer, ItemStack i
 
     public Map<String, Object> toMap(Action action){
 
-        if (action.getWorkflowId() != null) {
-            map = toMap(TAG_WORKFLOW_ID, action.getWorkflowId(), action.getName());
-        }
-
-        if (action.getGuidelineId() != null) {
-            map = toMap(TAG_GUIDELINE_ID, action.getGuidelineId(), action.getName());
-        }
-
         if (action.getTime() != null && !action.getTime().equals(new DvDateTime())) {
                 map = toMap(TAG_TIME, action.getTime(), action.getName());
         }

diff --git a/...ase/serialisation/flatencoding/std/marshal/postprocessor/ElementMarshalPostprocessor.java b/...ase/serialisation/flatencoding/std/marshal/postprocessor/ElementMarshalPostprocessor.java
@@ -38,6 +38,12 @@ public void process(
 
       handleRmAttribute(term, rmObject.getNullFlavour(), values, context, "null_flavour");
     }
+
+    if (rmObject.getNullReason() != null) {
+
+      handleRmAttribute(term, rmObject.getNullReason(), values, context, "null_reason");
+    }
+
   }
 
   /** {@inheritDoc} */

diff --git a/...g/ehrbase/serialisation/flatencoding/std/umarshal/postprocessor/ElementPostprocessor.java b/...g/ehrbase/serialisation/flatencoding/std/umarshal/postprocessor/ElementPostprocessor.java
@@ -20,6 +20,8 @@
 package org.ehrbase.serialisation.flatencoding.std.umarshal.postprocessor;
 
 import com.nedap.archie.rm.datastructures.Element;
+import com.nedap.archie.rm.datavalues.DvCodedText;
+import com.nedap.archie.rm.datavalues.DvText;
 import org.apache.commons.lang3.StringUtils;
 import org.ehrbase.client.classgenerator.shareddefinition.NullFlavour;
 import org.ehrbase.serialisation.walker.Context;
@@ -42,6 +44,18 @@ public void process(
       Set<String> consumedPaths,
       Context<Map<FlatPathDto, String>> context) {
 
+      Map<FlatPathDto, String> reasonValues = FlatHelper.filter(values, term + "/_null_reason", false);
+
+      if(!reasonValues.isEmpty()){
+
+        if(  FlatHelper.isDvCodedText(reasonValues,term + "_null_reason")){
+            rmObject.setNullReason(new DvCodedText());
+      } else {
+        rmObject.setNullReason(new DvText());
+          }
+      handleRmAttribute(term,rmObject.getNullReason(),reasonValues,consumedPaths,context,"null_reason");
+      }
+
     setValue(
         term + PATH_DIVIDER + "_null_flavour",
         "value",

diff --git a/...ion_conformance_test/src/test/java/org/ehrbase/conformance_test/db/DbConformanceTest.java b/...ion_conformance_test/src/test/java/org/ehrbase/conformance_test/db/DbConformanceTest.java
diff --git a/...rc/main/java/org/ehrbase/test_data/composition/CompositionTestDataConformanceSDTJson.java b/...rc/main/java/org/ehrbase/test_data/composition/CompositionTestDataConformanceSDTJson.java
@@ -136,6 +136,14 @@ public enum CompositionTestDataConformanceSDTJson implements CompositionTestData
           "ehrbase_conformance_admin_entry",
           "ehrbase_conformance_admin_entry.json",
           OperationalTemplateTestData.CONFORMANCE),
+  EHRBASE_CONFORMANCE_FEEDER_AUDIT_MULTIMEDIA(
+          "ehrbase_conformance_feeder_audit_multimedia",
+          "ehrbase_conformance_feeder_audit_multimedia.json",
+          OperationalTemplateTestData.CONFORMANCE),
+  EHRBASE_CONFORMANCE_SECTION(
+          "ehrbase_conformance_section",
+          "ehrbase_conformance_section.json",
+          OperationalTemplateTestData.CONFORMANCE),
   EHRBASE_CONFORMANCE_ELEMENT_FEEDER_AUDIT(
           "ehrbase_conformance_Element_feeder_audit",
           "ehrbase_conformance_Element_feeder_audit.json",

diff --git a/.../src/main/resources/composition/flat/simSDT/ehrbase_conformance_Element_feeder_audit.json b/.../src/main/resources/composition/flat/simSDT/ehrbase_conformance_Element_feeder_audit.json
@@ -17,6 +17,10 @@
   "conformance-ehrbase.de.v0/context/setting|terminology": "openehr",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|magnitude": 65.9,
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|unit": "unit",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_uid":"9fcc1c70-9349-444d-b9cb-8fa817697f5e",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_link:0|type": "problem",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_link:0|meaning": "problem related note",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_link:0|target": "ehr://ehr.network/347a5490-55ee-4da9-b91a-9bba710f730e",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_feeder_audit/originating_system_audit|version_id": "final",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_feeder_audit/originating_system_audit|system_id": "orig",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_feeder_audit/originating_system_audit/location|id": "12342341",

diff --git a/...a/src/main/resources/composition/flat/simSDT/ehrbase_conformance_Element_null_flavor.json b/...a/src/main/resources/composition/flat/simSDT/ehrbase_conformance_Element_null_flavor.json
@@ -18,6 +18,7 @@
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_null_flavour|code": "253",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_null_flavour|value": "unknown",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_null_flavour|terminology": "openehr",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_null_reason": "sample reason",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/time": "2021-12-21T16:02:58.0094262+01:00",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|code": "en",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|terminology": "ISO_639-1",

diff --git a/test-data/src/main/resources/composition/flat/simSDT/ehrbase_conformance_action.json b/test-data/src/main/resources/composition/flat/simSDT/ehrbase_conformance_action.json
@@ -48,5 +48,42 @@
   "conformance-ehrbase.de.v0/conformance_section/conformance_action/_work_flow_id|namespace": "HOSPITAL-NS",
   "conformance-ehrbase.de.v0/conformance_section/conformance_action/_work_flow_id|id": "335645",
   "conformance-ehrbase.de.v0/conformance_section/conformance_action/_work_flow_id|id_scheme": "HOSPITAL-NS",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_uid":"9fcc1c70-9349-444d-b9cb-8fa817697f5e",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_link:0|type": "problem",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_link:0|meaning": "problem related note",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_link:0|target": "ehr://ehr.network/347a5490-55ee-4da9-b91a-9bba710f730e",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit|version_id": "final",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit|system_id": "orig",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/location|id": "12342341",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/location|id_namespace": "uk.org.nmc",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/location|id_scheme": "NMC",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/location|name": "Org 1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/subject|id": "456",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/subject|id_namespace": "uk.org.nmc",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/subject|id_scheme": "NMC",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/subject|name": "Per 1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/provider|id": "456",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/provider|id_namespace": "uk.org.nmc",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/provider|id_scheme": "NMC",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit/provider|name": "Per 1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_audit|time": "2021-12-21T16:02:58.0094262+01:00",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:0|id": "id1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:0|issuer": "issuer1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:0|assigner": "assigner1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:0|type": "PERSON",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:1|id": "id2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:1|issuer": "issuer2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:1|assigner": "assigner2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/originating_system_item_id:1|type": "PERSON",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/original_content": "Hello world!",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/original_content|formalism": "text/plain",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:0|id": "id1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:0|issuer": "issuer1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:0|assigner": "assigner1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:0|type": "PERSON",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:1|id": "id2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:1|issuer": "issuer2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:1|assigner": "assigner2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_action/_feeder_audit/feeder_system_item_id:1|type": "PERSON",
   "conformance-ehrbase.de.v0/composer|name": "Silvia Blake"
 }
diff --git a/test-data/src/main/resources/composition/flat/simSDT/ehrbase_conformance_admin_entry.json b/test-data/src/main/resources/composition/flat/simSDT/ehrbase_conformance_admin_entry.json
@@ -36,5 +36,42 @@
   "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_work_flow_id|namespace": "HOSPITAL-NS",
   "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_work_flow_id|id": "335645",
   "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_work_flow_id|id_scheme": "HOSPITAL-NS",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_uid":"9fcc1c70-9349-444d-b9cb-8fa817697f5e",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_link:0|type": "problem",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_link:0|meaning": "problem related note",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_link:0|target": "ehr://ehr.network/347a5490-55ee-4da9-b91a-9bba710f730e",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit|version_id": "final",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit|system_id": "orig",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/location|id": "12342341",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/location|id_namespace": "uk.org.nmc",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/location|id_scheme": "NMC",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/location|name": "Org 1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/subject|id": "456",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/subject|id_namespace": "uk.org.nmc",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/subject|id_scheme": "NMC",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/subject|name": "Per 1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/provider|id": "456",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/provider|id_namespace": "uk.org.nmc",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/provider|id_scheme": "NMC",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit/provider|name": "Per 1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_audit|time": "2021-12-21T16:02:58.0094262+01:00",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:0|id": "id1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:0|issuer": "issuer1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:0|assigner": "assigner1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:0|type": "PERSON",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:1|id": "id2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:1|issuer": "issuer2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:1|assigner": "assigner2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/originating_system_item_id:1|type": "PERSON",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/original_content": "Hello world!",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/original_content|formalism": "text/plain",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:0|id": "id1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:0|issuer": "issuer1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:0|assigner": "assigner1",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:0|type": "PERSON",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:1|id": "id2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:1|issuer": "issuer2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:1|assigner": "assigner2",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/_feeder_audit/feeder_system_item_id:1|type": "PERSON",
   "conformance-ehrbase.de.v0/composer|name": "Silvia Blake"
 }
diff --git a/test-data/src/main/resources/composition/flat/simSDT/ehrbase_conformance_cluster.json b/test-data/src/main/resources/composition/flat/simSDT/ehrbase_conformance_cluster.json
@@ -49,6 +49,10 @@
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/conformance_cluster/_feeder_audit/feeder_system_item_id:1|issuer": "issuer2",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/conformance_cluster/_feeder_audit/feeder_system_item_id:1|assigner": "assigner2",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/conformance_cluster/_feeder_audit/feeder_system_item_id:1|type": "PERSON",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/conformance_cluster/_uid":"9fcc1c70-9349-444d-b9cb-8fa817697f5e",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/conformance_cluster/_link:0|type": "problem",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/conformance_cluster/_link:0|meaning": "problem related note",
+  "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/conformance_cluster/_link:0|target": "ehr://ehr.network/347a5490-55ee-4da9-b91a-9bba710f730e",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/time": "2021-12-21T16:02:58.0094262+01:00",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|code": "en",
   "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|terminology": "ISO_639-1",